MolecularPhylogenyandPopulationGeneticStructureofthe Shallow-waterSpinyLobsterPanulirushomarusintheSouth WestIndianOceanRegion:ImplicationsforManagement By MageshneeMayshreeReddy Submittedinfulfilmentoftheacademicrequirementsforthedegreeof MasterofScience(MarineBiology)intheSchoolofLifeSciences UniversityofKwaZulu-Natal,WestvilleCampus, Durban,SouthAfrica January2013 ABSTRACT Thescallopedspinylobster,Panulirushomarushasasubspeciestriothatarewidely distributedinshallow-waterhabitatsintheSouthWestIndianOcean.Subspeciesare definedbydifferencesincolourandabdominalsculpturalpattern.Aredvarietywiththe megasculpturalcarapacepattern,P.h.rubellusisdistributedalongthesoutheastcoast ofAfricaandMadagascar,wheretheyareendemic.AlongtheAfricancoastP.h. rubellusstockstraversepoliticalboundaries,MozambiqueandSouthAfrica.This projectaimedtofacilitateregionalfisheriesmanagementofsharedstocksbyemploying genetictoolstodeterminewhetherstocks(orpopulations)areindeedsharedbetween countries.Lobstersampleswerecollectedfromsevenlocalitiesthroughouttheeast Africancoast.Themitochondrialcyctochromecoxidasesubunit1regionwas sequencedtoassessthegeneticdiversity1)betweendifferentsubspecies,P.h.homarus andP.h.rubellusand2)betweenpopulationsofP.h.rubellusacrossitsAfrican distributionrange.UsingDNAbarcodingmethods,geneticdiversitywasalsofound betweenmorphologicallydistinctsubspecies,PanulirushomarushomarusandP.h. rubelluswhichdifferedgeneticallybyca.2-3%insequencedivergence.Both subspeciesweremonophyleticrelativetotheout-grouptaxaandformedwellsupported sisterclades(BI:1.00,ML:93%,P:100%,NJ:100%).ThedistributionofP.h. rubellusalongtheAfricancoastoccursadjacenttodifferentcurrentregimesand thereforevariedlarvaltransportmodes(i.e.AgulhasCurrentandinshorecounter- currentsalongtheEasternCape).Thismayhavedriventheformationofsubpopulations (ᶲPT=0.104,p=0.010)whichdifferbyca.1.7%insequencedifference.Thepatternof geneflowofpopulationsofP.h.rubelluslendssupporttotheAgulhasCurrentbeinga majormodeoflarvaltransportaswellascorroboratespreviousabundanceand distributionrecords.TimesincepopulationexpansionestimatesfortheP.h.homarus andP.h.rubellussubspeciesaswellasfortheP.h.rubellussubpopulationsdatedback tothemid-HoloceneEpochinaccordancewithawarmer,morestablemarine environment.GeneticallydistinctsubspeciesofP.homarusaswellasdifferentiated subpopulationsofP.h.rubelluscallsforare-visitofthecurrentcollectivemanagement ofP.homarusaswellasP.h.rubellusasasinglegeneticstockalongthesoutheast Africancoast. ii PREFACE TheexperimentalworkdescribedinthisdissertationwascarriedoutattheSchoolof LifeSciences,UniversityofKwaZulu-Natal,WestvilleCampus,Durban.Thiswas carriedoutunderthesupervisionofDrA.H.H.MacdonaldandProf.M.H.Schleyer. Thesestudiesrepresentoriginalworkbytheauthorandhavenototherwisebeen submittedinanyformforadegreeordiplomatoanytertiaryinstitution.Whereusehas beenmadeoftheworkofothers,itisdulynotedinthetext. Signed:.................................. Name:MissM.M.Reddy Date:22-01-2013 iii DECLARATION1–PLAGARISM I,MageshneeMayshreeReddydeclarethat: 1.Theresearchinthisthesis,exceptwhereotherwiseindicated,ismyoriginalresearch. 2.Thisdissertationhasnotbeensubmittedforanydegreeorexaminationatanyother University. 3.Thisthesisdoesnotcontainotherpersons’data,pictures,graphs,orotherinformation unlessspecificallyacknowledgedasbeingsourcedfromotherpersons. 4.Thisthesisdoesnotcontainotherpersons’writingunlessspecificallyacknowledged asbeingsourcedfromotherresearchers.Whereotherwrittensourceshavebeenquoted, then: a)Theirwordshavebeenre-writtenbutgeneralinformationattributedtothemhasbeen referenced. b)Wheretheirexactwordshavebeenused,thentheirwritinghasbeenplacedinitalics andinsidequotationmarks,andreferenced. 5.Thisdissertationdoesnotcontaintext,graphicsortablescopiedandpastedfromthe Internet,unlessspecificallyacknowledged,andthesourcebeingdetailedinthe dissertationandintheReferencessection. Signed:.................................. Name:MissM.M.Reddy Date:22-01-2013 iv DECLARATION2–CONFERENCEPRESENTATIONS 1.Reddy,M.M.,Macdonald,A.H.H.andSchleyer,M.H.2011.Areshallowwaterspiny lobster,PanulirushomaruspopulationsgeneticallystructuredorpanmiticintheSouth WestIndianOceanregion:Implicationsformanagement.7thWestIndianOceanMarine ScienceAssociation(WIOMSA)conference,Mombasa,Kenya. Authorcontribution:M.M.Reddydesignedthestudy,performedthelaboratorywork, developedthepresentationandpresentedthefinalproduct.A.H.H.Macdonaldand M.H.Schleyerco-authoredandprovidedoversightfortheproject. 2.Macdonald,A.H.H.,Chiazzari,B.,Reddy,M.M.,Kara,J.,Risi,M.,Escobar-Porras, J.,Montoya-Maya,P.,Zacarias,L.,Lamb,J.M.,Schleyer,M.H.andGroeneveld,J.C. 2012.MarinephylogeneticsattheUniversityofKwaZulu-Natal.10thSouthernAfrican SocietyforSystematicBiology(SASSBX)conference,Arniston,SouthAfrica. Authorcontribution:M.M.Reddydesignedandperformedthelaboratoryworkforan aspectoftheabovepresentationasdidtheotherauthors.A.H.H.Macdonalddeveloped thepresentationandpresentedthefinalproduct.M.H.Schleyer,J.M.LambandJ.C. Groeneveldco-authoredandprovidedsupervision. Signed:.................................. Name:MissM.M.Reddy Date:22-01-2013 v ACKNOWLEDGEMENTS Thisthesiswouldhavenotcometofruitionwithoutthehelpandsupportofanumberof people. Firstly,Iwouldliketosincerelythankmysupervisors,DrA.H.H.MacdonaldandProf. M.H.Schleyerfortheiracademicguidanceandrevisionofthemanuscript.Iwouldlike toalsothankDrJ.C.GroeneveldandProf.J.M.Lambforadditionalacademicadvice. Secondly,IhumblythanktheORIstaffandstudentsforassistanceinsamplingand guidanceinthefield;aspecialthankyoutoErikaSteynforassistinginorganisingfield trips,samplecollectionandidentificationoflobsters.IwouldalsoliketothankRuan vanderBergfromLiveFishTanks,WildCoastforthegenerousdonationoflobster muscletissue,DesmondHayesforassistanceinthefieldandLorencoZacariasfor samplecollectioninMozambique.IamalsogratefultoPhanorMontoya-Mayafor assistanceinadministrationandAlainSmithforassistanceingeneratingamapofthe studyarea. AbigthankyoutoTheshnieNaidoo,forassistanceinthelaboratory,guidanceon aspectsofthisprojectandConspec.foraccommodatingmeintheirlaboratory.Iam trulyindebtedtomyfamily(Mom,Dad,Verona,Vani,KonaandKyrah)andfriends (toomanytolist)foralltheirloveandsupportduringthecourseofmyMasters;anda specialthankyoutoDavidDyerforbeingareservoirofloveandsupport.Finally, thanksgototheNationalResearchFund(NRF)andSouthWestIndianOceanFisheries Project(SWIOFP)forfundingtheproject. vi CONTENTSPAGE CHAPTER1-BackgroundandRationale Background...............................................................................................................................2 Taxonomyandspeciesdescription........................................................................................2 Evolutionaryhistoryofthepalinurids..................................................................................3 Phylogenetics.........................................................................................................................4 Phylgeography.......................................................................................................................7 Distribution............................................................................................................................8 Ecology..................................................................................................................................8 Biology................................................................................................................................10 Growth.............................................................................................................................10 Sizeatsexualmaturity.....................................................................................................11 Reproduction....................................................................................................................12 Larvae..............................................................................................................................14 Populationgenetics.................................................................................................................16 Larvaldispersal....................................................................................................................16 Seascapegenetics................................................................................................................19 Molecularmarkers.................................................................................................................20 Applicationofmolecularmarkersinspinylobsters............................................................23 Taxonomyandsystematics..............................................................................................23 DNAbarcodingandthewideapplicationofCOI...........................................................24 Populationgeneticstudies................................................................................................26 Management...........................................................................................................................26 Thelobsterfishery...............................................................................................................27 ThePanulirushomarusfishery...........................................................................................28 Managementinsouthafrica................................................................................................28